workspace\(catalogs\)plink

PLINK Catalog

Description

Inventory and management utility for the PLINK executable used by genotype operations.

Details

Inventory and management utility for PLINK executables used by PolyGenius.

Use this catalog through workspace$catalogs$plink.

Behavior

  • Treats the manifest as read-only package data.

  • Detects the row compatible with the local operating system and CPU architecture.

  • Installs PLINK into the PolyGenius user cache, not into the package library.

  • Marks the active row dynamically from the current internal PLINK value.

Main methods

  • view(): manifest rows with compatible, installed, usable, and active status columns.

  • get(): return the active/compatible PLINK executable, optionally downloading it first.

  • set(): point the active session at a manually installed PLINK executable.

Methods

Public methods

Method new()

Initialize PLINK executable catalog.

Usage 
Plink$new(manifest.path = NULL)
Arguments
manifest.path

Optional custom manifest CSV path.

Method view()

View PLINK manifest rows with local installation status.

Usage 
Plink$view(os = NULL, arch = NULL, variant = NULL, version = NULL)
Arguments
os

Optional operating-system filter.

arch

Optional CPU architecture filter.

variant

Optional build variant filter.

version

Optional PLINK version filter.

Returns

data.frame inventory with compatibility and cache status flags.

Method get()

Get a PLINK executable path, optionally installing the compatible manifest row into the user cache first.

Usage 
Plink$get(
  os = NULL,
  arch = NULL,
  variant = NULL,
  version = NULL,
  install = TRUE,
  set.active = TRUE,
  quiet = TRUE,
  .execute = TRUE,
  .status = polygenius.option.execution.status()
)
Arguments
os

Optional operating-system filter. Defaults to the local OS.

arch

Optional CPU architecture filter. Defaults to the local architecture.

variant

Optional build variant filter. Defaults to “default”.

version

Optional PLINK version filter. Defaults to the newest compatible manifest version by manifest order.

install

Logical; when TRUE, download and cache the selected build if it is not already installed and usable.

set.active

Logical; when TRUE, set the selected executable as the active PLINK path for the current R session.

quiet

Logical; suppress progress messages from this method.

.execute

Logical; when TRUE, resolve the PLINK binary through the execution engine.

.status

Optional execution-status mode override (“auto”, “yes”, “no”).

Returns

Character scalar path to the PLINK executable, or NULL when no usable executable is available and install = FALSE.

Method add()

Add a local PLINK executable to the workspace cache.

Usage 
Plink$add(
  path,
  name = "local",
  version = "custom",
  os = NULL,
  arch = NULL,
  variant = "custom",
  set.active = TRUE,
  overwrite = FALSE
)
Arguments
path

Existing PLINK executable path.

name

Catalog name.

version

Version label.

os

Optional operating-system label. Defaults to local OS.

arch

Optional architecture label. Defaults to local architecture.

variant

Variant label.

set.active

Logical; activate the cached executable.

overwrite

Logical; overwrite an existing cached executable.

Returns

Cached executable path.

Method set()

Set the active PLINK executable path for the current R session.

Usage 
Plink$set(path, validate.version = TRUE)
Arguments
path

Existing PLINK executable path.

validate.version

Logical; when TRUE, run PLINK to verify it is usable before activating it.

Returns

Invisibly returns normalized path.

Method print()

Print PLINK inventory summary.

Usage 
Plink$print(...)
Arguments
…

Unused.

Returns

Invisibly returns self.